Yeah this question seems to come up a lot since the Family Guy episode where Peter asked this. Interestingly enough even though it's well known that Bob Saget is the voice of the Narrator he is not credited. No reason has been given so far as to why he is the Narrator. They have even shown Future Ted in the show and he sounds just like Present Ted.
My best guess is that this is a joke that was written and the punchline hasn't been revealed yet, a typical device for this show (such as what happened with the goat). It's supported by this story:
It was earlier speculated that Josh would replace Bob as the show's narrator for the finale, but executive producer Craig Thomas has reassured us that Bob isn't going anywhere for the finale.
Most likely there is a joke involved with the differences in voice.
Bob Saget is a well known name and many recognize his voice, which might be why he's used. It may have also contributed to the show getting green-lit, as there none of the cast was a big name actor at the time. Also, the distinction between future Ted's narration and the current story helps to differentiate between who is speaking at that moment. It would get confusing very quickly if present-day Ted's (Josh Radnor) voice were heard correcting his future-self. For the audience, it would be indistinguishable from the in-scene Ted.